GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

Authors: Chen, Hung-I Harry, Chiu, Yu-Chiao, Zhang, Tinghe, Zhang, Songyao, Huang, Yufei, Chen, Yidong

Source: BMC Systems Biology 2018, 12(Suppl 8):142

Subject Terms: Statistics - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1805.07874

Predicting drug response of tumors from integrated genomic profiles by deep neural networks

Authors: Chiu, Yu-Chiao, Chen, Hung-I Harry, Zhang, Tinghe, Zhang, Songyao, Gorthi, Aparna, Wang, Li-Ju, Huang, Yufei, Chen, Yidong

Subject Terms: Statistics - Machine Learning, Computer Science - Learning, Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1805.07702

Identification of functional genomic regions with copy number alteration in liver cancer

Authors: Hsiao, Tzu-Hung, Chen, Hung-I Harry, Chen, Yidong

Source: Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Genomic Signal Processing and Statistics, (GENSIPS), 2012 IEEE International Workshop on. :155-158 Dec, 2012

Relation: 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

Using gene sets to identify putative drugs for breast cancer

Authors: Hsiao, Tzu-Hung, Chen, Hung-I Harry, Chen, Yidong, Chen, Yu-Heng, Chuang, Eric Y.

Source: 2012 IEEE International Conference on Bioinformatics and Biomedicine Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on. :1-4 Oct, 2012

Relation: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

S-score: A novel scoring method of gene signatures for molecular classification

Authors: Chen, Hung-I Harry, Hsiao, Tzu-Hung, Chen, Yidong, Keller, Charles

Source: 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Genomic Signal Processing and Statistics (GENSIPS), 2011 IEEE International Workshop on. :154-157 Dec, 2011

Relation: 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

Gene sets enrichment analysis of miRNA expression profile

Authors: Hsiao, Tzu-Hung, Chen, Hung-I Harry, Sanchez-Diaz, Patricia C., Hung, Jaclyn Y., Chen, Yidong, Huang, Yufei

Source: 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on. :449-454 Nov, 2011

Relation: 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

A computational framework for predicting drug Mode-of-Action

Authors: Ma, Chifeng, Chen, Hung-I Harry, Huang, Yufei, Chen, Yidong

Source: 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference on. :374-379 Dec, 2010

Relation: 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

Deep learning of pharmacogenomics resources: moving towards precision oncology

Authors: Chiu, Yu-Chiao, Chen, Hung-I Harry, Gorthi, Aparna, Mostavi, Milad, Zheng, Siyuan, Huang, Yufei, Chen, Yidong

Source: Briefings in bioinformatics. 21(6):2066-2083

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132448877.0x000001&indx=1&recIds=ETOCvdc_100132448877.0x000001

Utilizing Cancer - Functional Gene Set - Compound Networks to Identify Putative Drugs for Breast Cancer

Authors: Hsiao, Tzu-Hung, Chiu, Yu-Chiao, Chen, Yu-Heng, Hsu, Yu-Ching, Chen, Hung-I Harry, Chuang, Eric Y., Chen, Yidong

Source: Combinatorial chemistry & high throughput screening. 21(2):74-83

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100078024723.0x000001&indx=1&recIds=ETOCvdc_100078024723.0x000001

Deep learning of pharmacogenomics resources: moving towards precision oncology.

Authors: Chiu, Yu-Chiao¹ (AUTHOR), Chen, Hung-I Harry^1,2 (AUTHOR), Gorthi, Aparna¹ (AUTHOR), Mostavi, Milad^1,2 (AUTHOR), Zheng, Siyuan^1,3 (AUTHOR), Huang, Yufei^2,3 (AUTHOR) Yufei.Huang@utsa.edu, Chen, Yidong^1,3 (AUTHOR) ChenY8@uthscsa.edu

Source: Briefings in Bioinformatics. Nov2020, Vol. 21 Issue 6, p2066-2083. 18p.

Subject Terms: *DEEP learning, *PHARMACOGENOMICS, *TUMOR classification, *GENOMICS, *ONCOLOGY, *CELL lines

Evidence for an Unanticipated Relationship between Undifferentiated Pleomorphic Sarcoma and Embryonal Rhabdomyosarcoma

Authors: Rubin, Brian P., Nishijo, Koichi, Chen, Hung-I Harry, Yi, Xiaolan, Schuetze, David P., Pal, Ranadip, Prajapati, Suresh I., Abraham, Jinu, Arenkiel, Benjamin R., Chen, Qing-Rong, Davis, Sean, McCleish, Amanda T., Capecchi, Mario R., Michalek, Joel E., Zarzabal, Lee Ann, Khan, Javed, Yu, Zhongxin, Parham, David M., Barr, Frederic G., Meltzer, Paul S., Chen, Yidong, Keller, Charles

Source: In Cancer Cell 2011 19(2):177-191

Correction to: Predicting drug response of tumors from integrated genomic profiles by deep neural networks

Authors: Chiu, Yu-Chiao, Chen, Hung-I Harry, Zhang, Tinghe, Zhang, Songyao, Gorthi, Aparna, Wang, Li-Ju, Huang, Yufei, Chen, Yidong

Source: BMC medical genomics. 12(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127205135.0x000001&indx=1&recIds=ETOCvdc_100127205135.0x000001

Predicting drug response of tumors from integrated genomic profiles by deep neural networks

Authors: Chiu, Yu-Chiao, Chen, Hung-I Harry, Zhang, Tinghe, Zhang, Songyao, Gorthi, Aparna, Wang, Li-Ju, Huang, Yufei, Chen, Yidong

Source: BMC medical genomics. 12

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127204859.0x000001&indx=1&recIds=ETOCvdc_100127204859.0x000001

CeL-ID: cell line identification using RNA-seq data

Authors: Mohammad, Tabrez A., Tsai, Yun S., Ameer, Safwa, Chen, Hung-I Harry, Chiu, Yu-Chiao, Chen, Yidong

Source: BMC genomics. 20

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127146980.0x000001&indx=1&recIds=ETOCvdc_100127146980.0x000001

Detection of high variability in gene expression from single-cell RNA-seq profiling.

Authors: Chen, Hung-I Harry^1,2, Yufang Jin², Yufei Huang² yufei.huang@utsa.edu, Yidong Chen^1,3 cheny8@uthscsa.edu

Source: BMC Genomics. 8/22/2016, Vol. 17, p119-128. 10p. 1 Diagram, 3 Charts, 4 Graphs.

Subject Terms: *GENE expression, *RNA sequencing, *ROOT-mean-squares, *NEGATIVE binomial distribution, *GENETIC regulation

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads.

Authors: Chen, Hung-I Harry^1,2, Yuanhang Liu^1,3, Yi Zou¹, Zhao Lai¹, Sarkar, Devanand^4,5, Yufei Huang², Yidong Chen^1,6 cheny8@uthscsa.edu

Source: BMC Genomics. 2015 Suppl 7, Vol. 16, p1-13. 13p. 2 Diagrams, 4 Charts, 4 Graphs.

Subject Terms: *RNA sequencing, *POISSON distribution, *BINOMIAL distribution, *EXONS (Genetics), *ANALYTIC mappings

A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.

Authors: Chen, Hung-I Harry, Hsu, Fang-Han, Jiang, Yuan

Source: Bioinformatics; August 15 2008, Vol. 24 Issue 16, p1749-1756, 8p

Antibody-mediated inhibition of GDF15–GFRAL activity reverses cancer cachexia in mice

Authors: Suriben, Rowena, Chen, Michael, Higbee, Jared, Oeffinger, Julie, Ventura, Richard, Li, Betty, Mondal, Kalyani, Gao, Zhengyu, Ayupova, Dina, Taskar, Pranali, Li, Diana, Starck, Shelley R., Chen, Hung-I Harry, McEntee, Michele, Katewa, Subhash D., Phung, Van, Wang, Marilyn, Kekatpure, Avantika, Lakshminarasimhan, Damodharan, White, Andre, Olland, Andrea, Haldankar, Raj, Solloway, Mark J., Hsu, Jer-Yuan, Wang, Yan, Tang, Jie, Lindhout, Darrin A., Allan, Bernard B.

Source: Nature Medicine; August 2020, Vol. 26 Issue: 8 p1264-1270, 7p

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